You may see a warning message like the one above when compiling your Intel® Stratix® 10 design in the Intel Quartus® Prime Pro software version 17.0 and later. The warning message may refer to one of the MSEL (0..2) pins and an SDM_IO function that is being used on that pin (e.g. CONF_DONE, INIT_DONE, HPS_COLD_RESET, HPS_WARM_RESET etc)
There is no requirement to make any internal connection to this pin and this warning message can be safely ignored.
This warning message can be safely ignored. It will be removed in a future release of the Intel Quartus Prime Pro software.